When the X-rays blast electrons out of one atom, stripping it from the inside out, it steals more from its neighbors – a new insight that could help advance high-resolution imaging of whole viruses, bacteria and complex materials.

With the most highly focused power of the world’s most powerful X-ray laser, scientists from a number of institutions around the world – including the U.S. Department of Energy’s (DOE) Argonne National Laboratory – have conducted a new experiment that takes apart molecules electron by electron.

“The key to this experiment was being able to focus hard X-rays to a very tiny spot.”

The results of this experiment, carried out at DOE’s SLAC National Accelerator Laboratory and published today in Nature, showed a surprising effect at the atomic scale. The researchers saw that a single laser pulse stripped all but a few electrons out of the molecule’s biggest atom, leaving a void that started pulling in electrons from the rest of the molecule, like a black hole gobbling a spiraling disk of matter. Within 30 femtoseconds – millionths of a billionth of a second – the molecule lost more than 50 electrons, far more than scientists anticipated based on earlier experiments using less intense beams or isolated atoms. Then it blew up.

“The key to this experiment was being able to focus hard X-rays to a very tiny spot,” said Argonne scientist Linda Young, an author of the study. “By concentrating the X-rays on a single atom in a molecule, we can see and even predict – on a very fast time scale – the electron movement between different atoms in the molecule and track unusual behaviors.”

“This paper shows that we can understand and model the radiation damage in small molecules, so now we can predict what damage we will get in other systems,” added Daniel Rolles of Kansas State University, another author of the study.

The experiment gives scientists fundamental insights they need to better plan and interpret experiments using intense and energetic X-ray pulses, like those created by the free-electron X-ray laser at the Linac Coherent Light Source at SLAC. Experiments that require these ultrahigh intensities include attempts to image individual biological objects, such as viruses and bacteria, at high resolution. They are also used to study the behavior of matter under extreme conditions, and to better understand charge dynamics in complex molecules.

The work represents a follow-on to an earlier experiment carried out by Young and other collaborators in 2010. The current experiment involves a much tighter focus of the X-ray energy, producing roughly 100 times higher intensity than previously achieved.

The current study also involved a significant theoretical component. “Because this experiment involves such high intensities and so many electrons, the theory is quite elaborate – you must calculate many different trajectories on the fly for multiple electronic configurations and molecular geometries. Because everything is happening on the same ultrafast time scale, it’s quite challenging,” Young said.

Like focusing the sun onto a thumbnail

The experiment, led by Rolles and Artem Rudenko of Kansas State, took place at LCLS’s Coherent X-ray Imaging (CXI) instrument. CXI delivers X-rays with the highest possible intensities achievable at LCLS and records data from samples in the instant before the laser pulse destroys them.

How intense are those X-ray pulses?

“They are about a hundred times more intense than what you would get if you focused all the sunlight that hits the Earth’s surface onto a thumbnail,” said LCLS staff scientist and co-author Sebastien Boutet.

For this study, researchers used special mirrors to focus the X-ray beam into a spot just over 100 nanometers in diameter – about a hundredth the size of the one used in most CXI experiments, and a thousand times smaller than the width of a human hair. They looked at three types of samples: individual xenon atoms, which have 54 electrons each, and two types of molecules that each contain a single iodine atom, which has 53 electrons.

Heavy atoms around this size are important in biochemical reactions, and researchers sometimes add them to biological samples to enhance contrast for imaging and crystallography applications. But until now, no one had investigated how the ultra-intense CXI beam affects molecules with atoms this heavy.

X-rays trigger electron cascades

The team tuned the energy of the CXI pulses so they would selectively strip the innermost electrons from the xenon or iodine atoms, creating “hollow atoms.” Based on earlier studies with less energetic X-rays, they thought cascades of electrons from the outer parts of the atom would drop down to fill the vacancies, only to be kicked out themselves by subsequent X-rays. That would leave just a few of the most tightly bound electrons. And, in fact, that’s what happened in both the freestanding xenon atoms and the iodine atoms in the molecules.

But in the molecules, the process didn’t stop there. The iodine atom, which had a strong positive charge after losing most of its electrons, continued to suck in electrons from neighboring carbon and hydrogen atoms, and those electrons were also ejected, one by one.

Rather than losing 47 electrons, as would be the case for an isolated iodine atom, the iodine in the smaller molecule lost 54, including the ones it grabbed from its neighbors – a level of damage and disruption that’s not only higher than would normally be expected, but significantly different in nature.

Results feed into theory to improve experiments

“We think the effect was even more important in the larger molecule than in the smaller one, but we don’t know how to quantify it yet,” Rudenko said. “We estimate that more than 60 electrons were kicked out, but we don’t actually know where it stopped because we could not detect all the fragments that flew off as the molecule fell apart to see how many electrons were missing. This is one of the open questions we need to study.”

For the data analyzed to date, the theoretical model provided excellent agreement with the observed behavior, providing confidence that more complex systems can now be studied, said LCLS director Mike Dunne. “This has important benefits for scientists wishing to achieve the highest-resolution images of biological molecules to inform the development of better pharmaceuticals, for example," he said. "These experiments will also guide the development of a next-generation instrument for the LCLS-II upgrade project, which will provide a major leap in capability due to the increase in repetition rate from 120 pulses per second to 1 million.”

The theory work for the study was led by Robin Santra of the Center for Free-Electron Laser Science at DESY and the University of Hamburg in Germany. Other research institutions contributing to the study were Tohoku University in Japan; Max Planck Institute for Nuclear Physics, Max Planck Institute for Medical Research, Hamburg Center for Ultrafast Imaging and the National Metrology Institute (PTB) in Germany; the University of Science and Technology in Beijing; Aarhus University in Denmark; Sorbonne University in France; the DOE’s Argonne National Laboratory and Brookhaven National Laboratory; the University of Chicago; Kansas State University; and Northwestern University. Funding for the research came from the DOE Office of Science [Basic Energy Sciences, Chemical Sciences, Geosciences and Biosciences Division] and from the German Research Foundation (DFG).

LCLS is a DOE Office of Science User Facility.

SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the U.S. Department of Energy Office of Science. To learn more, please visit www.slac.stanford.edu.

SLAC National Accelerator Laboratory is supported by the Office of Science of the U.S. Department of Energy. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science.

The U.S. Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit the Office of Science website.

--By Jared Sagoff and Andrew Gordon.

A team of researchers, including several physicists from the U.S. Department of Energy’s Argonne National Laboratory, discovered that a molecule containing a large atom could act like a molecular “black hole” when exposed to ultrafast laser pulses, sucking in electrons from nearby lighter atoms. (Image courtesy of DESY). (Image courtesy of DESY.)

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